Locking-Proof Tetrahedra

The simulation of incompressible materials suffers from locking when using the standard finite element method (FEM) and coarse linear tetrahedral meshes. Locking increases as the Poisson ratio gets close to 0.5 and often lower Poisson ratio values are used to reduce locking, affecting volume preservation. We propose a novel mixed FEM approach to simulating incompressible solids that alleviates the locking problem for tetrahedra. Our method uses linear shape functions for both displacements and pressure, and adds one scalar per node. It can accommodate nonlinear isotropic materials described by a Young\u27s modulus and any Poisson ratio value by enforcing a volumetric constitutive law. The most realistic such material is Neo-Hookean, and we focus on adapting it to our method. For , we can obtain full volume preservation up to any desired numerical accuracy. We show that standard Neo-Hookean simulations using tetrahedra are often locking, which, in turn, affects accuracy. We show that our method gives better results and that our Newton solver is more robust. As an alternative, we propose a dual ascent solver that is simple and has a good convergence rate. We validate these results using numerical experiments and quantitative analysis

Collision Detection and Merging of Deformable B-Spline Surfaces in Virtual Reality Environment

This thesis presents a computational framework for representing, manipulating and merging rigid and deformable freeform objects in virtual reality (VR) environment. The core algorithms for collision detection, merging, and physics-based modeling used within this framework assume that all 3D deformable objects are B-spline surfaces. The interactive design tool can be represented as a B-spline surface, an implicit surface or a point, to allow the user a variety of rigid or deformable tools. The collision detection system utilizes the fact that the blending matrices used to discretize the B-spline surface are independent of the position of the control points and, therefore, can be pre-calculated. Complex B-spline surfaces can be generated by merging various B-spline surface patches using the B-spline surface patches merging algorithm presented in this thesis. Finally, the physics-based modeling system uses the mass-spring representation to determine the deformation and the reaction force values provided to the user. This helps to simulate realistic material behaviour of the model and assist the user in validating the design before performing extensive product detailing or finite element analysis using commercially available CAD software. The novelty of the proposed method stems from the pre-calculated blending matrices used to generate the points for graphical rendering, collision detection, merging of B-spline patches, and nodes for the mass spring system. This approach reduces computational time by avoiding the need to solve complex equations for blending functions of B-splines and perform the inversion of large matrices. This alternative approach to the mechanical concept design will also help to do away with the need to build prototypes for conceptualization and preliminary validation of the idea thereby reducing the time and cost of concept design phase and the wastage of resources

Fast Volume Rendering and Deformation Algorithms

Volume rendering is a technique for simultaneous visualization of surfaces and inner structures of objects. However, the huge number of volume primitives (voxels) in a volume, leads to high computational cost. In this dissertation I developed two algorithms for the acceleration of volume rendering and volume deformation. The first algorithm accelerates the ray casting of volume. Previous ray casting acceleration techniques like space-leaping and early-ray-termination are only efficient when most voxels in a volume are either opaque or transparent. When many voxels are semi-transparent, the rendering time will increase considerably. Our new algorithm improves the performance of ray casting of semi-transparently mapped volumes by exploiting the opacity coherency in object space, leading to a speedup factor between 1.90 and 3.49 in rendering semi-transparent volumes. The acceleration is realized with the help of pre-computed coherency distances. We developed an efficient algorithm to encode the coherency information, which requires less than 12 seconds for data sets with about 8 million voxels. The second algorithm is for volume deformation. Unlike the traditional methods, our method incorporates the two stages of volume deformation, i.e. deformation and rendering, into a unified process. Instead to deform each voxel to generate an intermediate deformed volume, the algorithm follows inversely deformed rays to generate the desired deformation. The calculations and memory for generating the intermediate volume are thus saved. The deformation continuity is achieved by adaptive ray division which matches the amplitude of local deformation. We proposed approaches for shading and opacit adjustment which guarantee the visual plausibility of deformation results. We achieve an additional deformation speedup factor of 2.34~6.58 by incorporating early-ray-termination, space-leaping and the coherency acceleration technique in the new deformation algorithm

Modelling and Animation using Partial Differential Equations. Geometric modelling and computer animation of virtual characters using elliptic partial differential equations.

This work addresses various applications pertaining to the design, modelling and animation of parametric surfaces using elliptic Partial Differential Equations (PDE) which are produced via the PDE method. Compared with traditional surface generation techniques, the PDE method is an effective technique that can represent complex three-dimensional (3D) geometries in terms of a relatively small set of parameters. A PDE-based surface can be produced from a set of pre-configured curves that are used as the boundary conditions to solve a number of PDE. An important advantage of using this method is that most of the information required to define a surface is contained at its boundary. Thus, complex surfaces can be computed using only a small set of design parameters. In order to exploit the advantages of this methodology various applications were developed that vary from the interactive design of aircraft configurations to the animation of facial expressions in a computer-human interaction system that utilizes an artificial intelligence (AI) bot for real time conversation. Additional applications of generating cyclic motions for PDE based human character integrated in a Computer-Aided Design (CAD) package as well as developing techniques to describe a given mesh geometry by a set of boundary conditions, required to evaluate the PDE method, are presented. Each methodology presents a novel approach for interacting with parametric surfaces obtained by the PDE method. This is due to the several advantages this surface generation technique has to offer. Additionally, each application developed in this thesis focuses on a specific target that delivers efficiently various operations in the design, modelling and animation of such surfaces.The project files will not be available online

Parametric design and optimization of arched trusses under vertical and horizontal multi-load cases

This dissertation faces the problem of the optimum design of steel truss arches subject to multiple load cases. Arches are one of the most ancient shape-resistant structures, widely used in both civil engineering and architecture. For instance, arches can be considered as purely compressed structures, provided that their “line of thrust” coincides with the centre line of the arch. The “line of thrust” is the locus of the points of application of the thrusts (internal forces or stress resultants) that must be contained within the cross-section of the arch in such a way that the arch transfers loads to the foundations through axial compressive stresses only. As a matter of fact, the more the “line of thrust” differs from the centre line of the arch, the larger the unfavourable bending moments that arise in the arch. This is the reason why it is fundamental to pay close attention to the choice of the shape for an arch in order to minimize (or avoid when it is possible) unfavourable bending effects. Several analytical, graphical and physical methods are provided to find the optimal shape of a monolithic (single rib) arch subjected to a certain load case (i.e. the “funicular curve” for that load). However, if multiple load cases must be considered, it is not possible to find a proper optimal shape for an arch with single rib. In this case, the choice of truss arches with at least two chords becomes indispensable. Indeed, it has been demonstrated that structural optimization of in-plane truss arches with two chords subjected to a single load case leads to optimal solutions in which upper and lower chords tend to coincide with each other and with the “funicular curve” (i.e. the “line of thrust”) for that load. In light of the above, simultaneous shape and size optimization of steel truss arches with two arched chords linked each other through a bracing system (with variable Pratt-type pattern) has been performed for multiple load cases and different structural boundary conditions. Truss arches are effectively used in arch bridges, especially when the arch span exceeds 200 meters (five out of the six steel arch bridges with a span over 500 m are truss arch bridges). For this purpose, a hybrid optimization routine integrating a parametric definition of the design problem, a metaheuristic optimization algorithm and a code for Finite Element Analysis (FEA) has been developed through a MATLAB program. The proposed optimization method allows to simultaneously optimize a larger set of design variables, notwithstanding their large number and various nature (topology, shape and size, as well as continuous and discrete variables, have been concurrently considered). Third-degree Rational Bézier Curves have been chosen to optimize the shape of the arch chords because they can represent a wide family of curves (including conic curves), depending on a small number of parameters. In so doing, in-plane truss arches with different span lengths and structural boundary conditions have been optimized for multiple load cases, only considering vertical loads (acting on the same plane as the arch), since in-plane arches are not suited to withstand out-of-plane loads. On the other hand, spatial arched trusses with two arched chords lying on different planes have been optimally designed for multiple loadings acting in different directions. In particular, a steel arched truss with a lower arched chord variably inclined in the 3D-space and a horizontal upper arched chord linked each other through a bracing system has been designed and optimized for three vertical load cases and a horizontal seismic action parallel to the upper chord plane. Thus, analysing the obtained results, useful suggestions for steel truss arch design have been deduced and presented in this dissertation

Integrated structural analysis using isogeometric finite element methods

The gradual digitization in the architecture, engineering, and construction industry over the past fifty years led to an extremely heterogeneous software environment, which today is embodied by the multitude of different digital tools and proprietary data formats used by the many specialists contributing to the design process in a construction project. Though these projects become increasingly complex, the demands on financial efficiency and the completion within a tight schedule grow at the same time. The digital collaboration of project partners has been identified as one key issue in successfully dealing with these challenges. Yet currently, the numerous software applications and their respective individual views on the design process severely impede that collaboration. An approach to establish a unified basis for the digital collaboration, regardless of the existing software heterogeneity, is a comprehensive digital building model contributed to by all projects partners. This type of data management known as building information modeling (BIM) has many benefits, yet its adoption is associated with many difficulties and thus, proceeds only slowly. One aspect in the field of conflicting requirements on such a digital model is the cooperation of architects and structural engineers. Traditionally, these two disciplines use different abstractions of reality for their models that in consequence lead to incompatible digital representations thereof. The onset of isogeometric analysis (IGA) promised to ease the discrepancy in design and analysis model representations. Yet, that initial focus quickly shifted towards using these methods as a more powerful basis for numerical simulations. Furthermore, the isogeometric representation alone is not capable of solving the model abstraction problem. It is thus the intention of this work to contribute to an improved digital collaboration of architects and engineers by exploring an integrated analysis approach on the basis of an unified digital model and solid geometry expressed by splines. In the course of this work, an analysis framework is developed that utilizes such models to automatically conduct numerical simulations commonly required in construction projects. In essence, this allows to retrieve structural analysis results from BIM models in a fast and simple manner, thereby facilitating rapid design iterations and profound design feedback. The BIM implementation Industry Foundation Classes (IFC) is reviewed with regard to its capabilities of representing the unified model. The current IFC schema strongly supports the use of redundant model data, a major pitfall in digital collaboration. Additionally, it does not allow to describe the geometry by volumetric splines. As the pursued approach builds upon a unique model for both, architectural and structural design, and furthermore requires solid geometry, necessary schema modifications are suggested. Structural entities are modeled by volumetric NURBS patches, each of which constitutes an individual subdomain that, with regard to the analysis, is incompatible with the remaining full model. The resulting consequences for numerical simulation are elaborated in this work. The individual subdomains have to be weakly coupled, for which the mortar method is used. Different approaches to discretize the interface traction fields are implemented and their respective impact on the analysis results is evaluated. All necessary coupling conditions are automatically derived from the related geometry model. The weak coupling procedure leads to a linear system of equations in saddle point form, which, owed to the volumetric modeling, is large in size and, the associated coefficient matrix has, due to the use of higher degree basis functions, a high bandwidth. The peculiarities of the system require adapted solution methods that generally cause higher numerical costs than the standard procedures for symmetric, positive-definite systems do. Different methods to solve the specific system are investigated and an efficient parallel algorithm is finally proposed. When the structural analysis model is derived from the unified model in the BIM data, it does in general initially not meet the requirements on the discretization that are necessary to obtain sufficiently accurate analysis results. The consequently necessary patch refinements must be controlled automatically to allowfor an entirely automatic analysis procedure. For that purpose, an empirical refinement scheme based on the geometrical and possibly mechanical properties of the specific entities is proposed. The level of refinement may be selectively manipulated by the structural engineer in charge. Furthermore, a Zienkiewicz-Zhu type error estimator is adapted for the use with isogeometric analysis results. It is shown that also this estimator can be used to steer an adaptive refinement procedure

Geometric modeling, simulation, and visualization methods for plasmid DNA molecules

Plasmid DNA molecules are a special type of DNA molecules that are used, among other applications, in DNA vaccination and gene therapy. These molecules are characterized by, when in their natural state, presenting a closed-circular conformation and by being supercoiled. The production of plasmid DNA using bacteria as hosts implies a purification step where the plasmid DNA molecules are separated from the DNA of the host and other contaminants. This purification process, and all the physical and chemical variations involved, such as temperature changes, may affect the plasmid DNA molecules conformation by uncoiling or even by open them, which makes them useless for therapeutic applications. Because of that, researchers are always searching for new purification techniques that maximize the amount of supercoiled plasmid DNA that is produced. Computer simulations and 3D visualization of plasmid DNA can bring many advantages because they allow researchers to actually see what can happen to the molecules under certain conditions. In this sense, it was necessary to develop reliable and accurate geometric models specific for plasmid DNA simulations. This dissertation presents a new assembling algorithm for B-DNA specifically developed for plasmid DNA assembling. This new assembling algorithm is completely adaptive in the sense that it allows researchers to assemble any plasmid DNA base-pair sequence along any arbitrary conformation that fits the length of the plasmid DNA molecule. This is specially suitable for plasmid DNA simulations, where conformations are generated by simulation procedures and there is the need to assemble the given base-pair sequence over that conformation, what can not be done by conventional predictive DNA assembling methods. Unlike traditional molecular visualization methods that are based on the atomic structure, this new assembling algorithm uses color coded 3D molecular surfaces of the nucleotides as the building blocks for DNA assembling. This new approach, not only reduces the amount of graphical objects and, consequently, makes the rendering faster, but also makes it easier to visually identify the nucleotides in the DNA strands. The algorithm used to triangulate the molecular surfaces of the nucleotides building blocks is also a novelty presented as part of this dissertation. This new triangulation algorithm for Gaussian molecular surfaces introduces a new mechanism that divides the atomic structure of molecules into boxes and spheres. This new space division method is faster because it confines the local calculation of the molecular surface to a specific region of influence of the atomic structure, not taking into account atoms that do not influence the triangulation of the molecular surface in that region. This new method also guarantees the continuity of the molecular surface. Having in mind that the aim of this dissertation is to present a complete set of methods for plasmid DNA visualization and simulation, it is also proposed a new deformation algorithm to be used for plasmid DNA Monte Carlo simulations. This new deformation algorithm uses a 3D polyline to represent the plasmid DNA conformation and performs small deformations on that polyline, keeping the segments length and connectivity. Experiments have been performed in order to compare this new deformation method with deformation methods traditionally used by Monte Carlo plasmid DNA simulations These experiments shown that the new method is more efficient in the sense that its trial acceptance ratio is higher and it converges sooner and faster to the elastic energy equilibrium state of the plasmid DNA molecule. In sum, this dissertation successfully presents an end-to-end set of models and algorithms for plasmid DNA geometric modelling, visualization and simulation